They probably aren't including the whale sharks because it's so expensive, but they do start to arrive around March (some friends from Denmark were lucky enough to dive with them in early March this year).
I have done the glass bottom boat a few times, and it seems strange you need to waitlist already. It's quite an inexpensive tour, if you book as a member of the public. It seems crazy that it is already 'booked out' b ut it might be because the tour company hasn't opened for bookings yet.
https://www.glassbottomboat.com.au/
Turquoise Bay is one of my most favourite beaches in the world. You don't even have to be a strong swimmer to enjoy it. Turquoise Bay is famous for drift snorkelling. Most people just lean over a swimming noodle and let the current take them out and then back in. You can see fish swimming around your feet etc because the reef there is protected as part of the national park.
https://exploreparks.dbca.wa.gov.au/site/turquoise-bay
How long do they give you in Exmouth? you could consider hiring a car and driving yourself to the boat ramp, and then to the National Park and Turquoise Bay.